title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1129 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A link: https://peerj.com/articles/9213 last-modified: 2020-05-20 description: IntroductionProphylactic vaccines are already available for prevention of human papillomavirus (HPV) infection. However, we still await development of therapeutic vaccines with high efficiency for stimulating specific T lymphocytes to clear HPV infection.ObjectiveThis study investigates the potential for subunits of human p16INK4a protein and E2 protein of HPV16 to stimulate dendritic cells and enhance the specific response of T lymphocytes against HPV-infected cells.MethodologyImmunogenic epitopes of HPV16 E2 and p16INK4a proteins were predicted through the common HLA class I and II alleles present in the Thai population. Then, monocyte-derived dendritic cells (MDCs) were pulsed with HPV16 E2 and/or p16INK4a protein s and their maturity assessed. MDCs pulsed with either or both of these proteins at optimal concentrations were used for activation of autologous T lymphocytes and IFN-γ production was measured for specific response function.ResultsHPV16 E2 and p16INK4a proteins contain various immunogenic epitopes which can be presented by antigen-presenting cells via both HLA class I and II molecules. The stimulation of MDCs with either HPV16 E2 or p16INK4a proteins increased percentages and mean fluorescence intensity (MFI) of CD83+ MDCs in a dose-dependent manner. An optimum concentration of 250 ng/mL and 150 ng/mL of HPV16 E2 and p16INK4a proteins, respectively, stimulated MDCs via the MAPK pathway (confirmed by use of MAPK inhibitors). T lymphocytes could be activated by MDCs pulsed with these proteins, leading to high percentages of both CD4+ IFN-γ+ T lymphocytes and CD8+ IFN-γ+ T lymphocytes. The production of IFN-γ was higher in co-cultures containing MDCs pulsed with HPV16 E2 protein than those pulsed with p16INK4a. Interestingly, MDCs pulsed with a combination of HPV16 E2 and p16INK4a significantly increased IFN-γ production of T lymphocytes. The IFN-γ production was inhibited by both HLA class I and II blockade, particularly in co-cultures with MDCs pulsed with a combination of HPV16 E2 and p16INK4a.ConclusionsThis suggests that MDCs pulsed with both proteins enhances specific response of both CD4+ and CD8+ T lymphocytes. This study might provide a strategy for further in vivo study of stimulation of T lymphocytes for therapy of HPV-associated cancer. creator: Nuchsupha Sunthamala creator: Neeranuch Sankla creator: Jureeporn Chuerduangphui creator: Piyawut Swangphon creator: Wanchareeporn Boontun creator: Supakpong Ngaochaiyaphum creator: Weerayut Wongjampa creator: Tipaya Ekalaksananan creator: Chamsai Pientong uri: https://doi.org/10.7717/peerj.9213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sunthamala et al. title: Non-parallel changes in songbird migration timing are not explained by changes in stopover duration link: https://peerj.com/articles/8975 last-modified: 2020-05-19 description: Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration—the time that individuals spend resting and refueling at a site—are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration—the number of days that a study site is occupied by a particular species—by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies. creator: Nicholas N. Dorian creator: Trevor L. Lloyd-Evans creator: J. Michael Reed uri: https://doi.org/10.7717/peerj.8975 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Dorian et al. title: Recent advances in biochar application for water and wastewater treatment: a review link: https://peerj.com/articles/9164 last-modified: 2020-05-19 description: In the past decade, researchers have carried out a massive amount of research on the application of biochar for contaminants removal from aqueous solutions. As an emerging sorbent with great potential, biochar has shown significant advantages such as the broad sources of feedstocks, easy preparation process, and favorable surface and structural properties. This review provides an overview of recent advances in biochar application in water and wastewater treatment, including a brief discussion of the involved sorption mechanisms of contaminants removal, as well as the biochar modification methods. Furthermore, environmental concerns of biochar that need to be paid attention to and future research directions are put forward to promote the further application of biochar in practical water and wastewater treatment. creator: Xiaoqing Wang creator: Zizhang Guo creator: Zhen Hu creator: Jian Zhang uri: https://doi.org/10.7717/peerj.9164 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The ability of oriental magpies (Pica serica) to solve baited multiple-string problems link: https://peerj.com/articles/9200 last-modified: 2020-05-19 description: BackgroundBaited multiple-string problems are commonly used in avian laboratory studies to evaluate complex cognition. Several bird species possess the ability to use a string pull for obtaining food.MethodsWe initially tested and trained 11 magpies to determine whether the oriental magpie (Pica sericia) possesses the ability to solve baited multiple-string problems. Eight of the birds obtained the bait by pulling, and were selected for formal multiple-string tasks in the second stage. Second stage tests were divided into seven tasks based on string configurations.ResultsOnly two magpies were able to solve two tasks: one solved the task of parallel strings, and the other solved the task of slanted strings with the bait farther from the middle point between the two strings and selected the short string in the task of long-short strings. When faced with more difficult tasks (i.e., the task of slanted strings with the bait closer to the middle point between the two strings, the task with two crossing strings, and the task of continuity and discontinuity), the birds initially observed the tasks and chose instead to adopt simpler strategies based on the proximity principle, side bias strategies and trial-and-error learning. Our results indicate that the oriental magpie had a partial understanding of the principle of multiple-string problems but adopted simpler strategies. creator: Lin Wang creator: Jinxin Guo creator: Heng jiu Tian creator: Jinling Sui uri: https://doi.org/10.7717/peerj.9200 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study link: https://peerj.com/articles/9212 last-modified: 2020-05-19 description: BackgroundEpidermal growth factor (EGF) is a pro-inflammatory small peptide that stimulates cell growth, proliferation and differentiation through binding to its receptor. EGF rs2237051 and serum EGF levels have been demonstrated to be related with a variety of diseases, including several tumors and inflammatory diseases. Therefore, this study aims to investigate the association of the EGF rs2237051 variant and serum EGF levels in Chinese patients with generalized aggressive periodontitis (GAgP).Material and MethodsA case-control study was conducted among 216 patients with GAgP and 138 healthy controls. The clinical parameters of plaque index, probing depth, attachment loss and bleeding index were recorded. The EGF rs2237051 polymorphism was genotyped using time-of-flight mass spectrometry, and serum EGF levels were determined. Logistic and linear regression models were used to investigate the association between the genotypes of EGF rs2237051, serum EGF levels and GAgP risk.ResultsThe AA genotype of EGF rs2237051 showed higher risk for GAgP than the combined genotypes GG and AG (adjusted OR = 1.65, 95% CI [1.06–2.57]). Increased serum EGF levels were associated with GAgP (adjusted OR = 1.18, 95% CI [1.14–1.22]). Moreover, the serum EGF level for the AA genotype was significantly higher than that for the AG/GG genotypes in patients with GAgP (adjusted β = 4.70, 95% CI [2.09–7.31]).ConclusionWe demonstrated that EGF rs2237051 variant and the increased level of serum EGF were associated with the risk of GAgP, the serum EGF was up-regulated in patients with GAgP. It was indicated that serum EGF might be a biomarker of GAgP and EGF rs2237051 may be related to the genetic background of GAgP. creator: Xian’e Wang creator: Wenjing Li creator: Li Xu creator: Ruifang Lu creator: Huanxin Meng uri: https://doi.org/10.7717/peerj.9212 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: The case for extended lifespan in cooperatively breeding mammals: a re-appraisal link: https://peerj.com/articles/9214 last-modified: 2020-05-19 description: Recent comparative studies have suggested that cooperative breeding is associated with increases in maximum lifespan among mammals, replicating a pattern also seen in birds and insects. In this study, we re-examine the case for increased lifespan in mammalian cooperative breeders by analysing a large dataset of maximum longevity records. We did not find any consistent, strong evidence that cooperative breeders have longer lifespans than other mammals after having controlled for variation in body mass, mode of life and data quality. The only possible exception to this general trend is found in the African mole-rats (the Bathyergid family), where all members are relatively long-lived, but where the social, cooperatively breeding species appear to be much longer-lived than the solitary species. However, solitary mole-rat species have rarely been kept in captivity or followed longitudinally in the wild and so it seems likely that their maximum lifespan has been underestimated when compared to the highly researched social species. Although few subterranean mammals have received much attention in a captive or wild setting, current data instead supports a causal role of subterranean living on lifespan extension in mammals. creator: Jack Thorley uri: https://doi.org/10.7717/peerj.9214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Thorley title: Plasma antioxidants and oxidative stress status in obese women: correlation with cardiopulmonary response link: https://peerj.com/articles/9230 last-modified: 2020-05-19 description: IntroductionA high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses in women of different body mass index (BMI).Subjects and MethodsEighty female adults were recruited and divided into three groups; normal weight (n = 23), overweight (n = 28) and obese (n = 29), according to their BMI. Blood samples were obtained prior to cardiopulmonary exercise testing. Plasma samples were separated by centrifugation and analysed for enzymatic antioxidant activity including catalase, glutathione peroxidase and superoxide dismutase. Non-enzymatic antioxidant activities were assessed using 2, 2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging and ferric reducing ability of plasma (FRAP) assays. To evaluate the oxidative stress status of subjects, levels of reactive oxygen species and malondialdehyde, the by-product of lipid peroxidation, were measured. Cardiopulmonary responses were analysed using cardiopulmonary exercise testing (CPET) which involved 15 various parameters such as peak oxygen consumption, metabolic equivalents and respiratory exchange ratio.ResultsThe obese group had significantly lower ABTS radical scavenging and FRAP activities than the normal weight group. A higher catalase activity was observed in the obese group than the normal weight group. Spearman’s correlation showed an inverse relationship between catalase and peak oxygen consumption, while partial correlation analysis showed inverse correlations between superoxide dismutase and respiratory frequency, ABTS activity and oxygen pulse, and between ABTS activity and cardiac output.ConclusionOur results demonstrate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase activity may be a compensatory mechanism. The negative correlations found between these two parameters may indicate the potential effect of antioxidants on the cardiopulmonary system and deserve further analysis in a larger population. Nevertheless, this study provides the basis for future studies to further explore the relationships between redox status and cardiopulmonary responses. This can potentially be used to predict future risk of developing diseases associated with oxidative stress, especially pulmonary and cardiovascular diseases. creator: Dyg Mastura Adenan creator: Zulkarnain Jaafar creator: Jaime Jacqueline Jayapalan creator: Azlina Abdul Aziz uri: https://doi.org/10.7717/peerj.9230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Adenan et al. title: Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi link: https://peerj.com/articles/9061 last-modified: 2020-05-18 description: The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria. creator: Yayuan Zhang creator: Jixiang Chen creator: Yonggang Wang creator: Yanlin Li creator: Wenhong Rui creator: Jiyi Zhang creator: Dan Luo uri: https://doi.org/10.7717/peerj.9061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: The influence of surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea link: https://peerj.com/articles/9101 last-modified: 2020-05-18 description: Wetland ecosystems have been globally degraded and lost due to rapid urbanization and climate change. An assessment of national scale inventory, including wetland types and conditions, is urgently required to understand the big picture of endangered wetlands, such as where they are and how they look like. We analyzed the spatial patterns of each inland wetland type (brackish wetland was included) in South Korea and the relative importance of land cover categories on wetland conditions. The wetlands were grouped into four dominant types (riverine, lake, mountain, and human-made) according to their topography. Riverine wetlands constituted the largest area (71.3%). The relative ratio of wetlands in a well-conserved condition (i.e., “A” rank) was highest in riverine wetlands (23.8%), followed by mountain wetlands (22.1%). The higher proportion of grasslands was related to a better condition ranking, but the increasing bareland area had a negative impact on wetland conditions. We also found that wetlands located near wetland protected areas tend to be in a better condition compared to remote sites. Our results further support the importance of the condition of surrounding areas for wetland conservation. creator: Ran-Young Im creator: Taekyu Kim creator: Chung-Yeol Baek creator: Chang-Su Lee creator: Song-Hyun Kim creator: Jung-Hwan Lee creator: Ji Yoon Kim creator: Gea-Jae Joo uri: https://doi.org/10.7717/peerj.9101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Im et al. title: Mitochondrial DNA variation in the Italian Heavy Draught Horse link: https://peerj.com/articles/8996 last-modified: 2020-05-15 description: BackgroundIn the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.MethodologyTo provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.ResultsAmong the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices. creator: Hovirag Lancioni creator: Irene Cardinali creator: Andrea Giontella creator: Maria Teresa Antognoni creator: Arianna Miglio uri: https://doi.org/10.7717/peerj.8996 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lancioni et al.